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Aloni began his career as a painter, establishing the Bugrashov gallery in Tel Aviv, a home for contemporary art, cultural and political events. While living in New York in the 1990s, his work in large-scale art led him to invent a method for advertising on urban architectural structures.

Aloni was the head cinema coach in the Freedom Theatre of the Jenin Refugee Camp. After the 2011 murder of Juliano Mer Khamis, the founder and head of The Freedom Theater, Aloni directed an Arabic adaptation of Waiting for Godot with the Freedom Theatre's graduate students, a production that toured to New York. He is a member of the advisory board of Jewish Voice for Peace, a Jewish organization based in the United States that advocates for a peaceful resolution of the Israeli-Arab conflict.

Aloni's book Gilgul Mechilot (Forgiveness, Or Rolling In the Underworld's Tunnels), a collection of stories and pensées, includes his politically charged essays Messianic Manifesto for Binationalism and Reflections on the Coming of the Messiah.[4] Aloni coined the phrases "radical leftist Messianism" and "radical grace" to describe his political ideology, which attempts to identify and analyze the theology of secularism, or the unconscious theological underpinnings of secularist and liberal discourses, specifically in Israel. In Messianic Manifesto for Binationalism,[4] he calls for a radical re-reading of Zionism, stating that "Any attempt to resist the Law of the Father as violent Zionist extremism only strengthens him. […] We must cleanse Zionism of its nationalistic elements without relinquishing its Messianic fervor for liberty, freedom, and equality."

Aloni promotes the concept of binationalism in Israel-Palestine, and he believes that fidelity to the Israeli people and fidelity to the Palestinian people are one and the same. He accuses the current Israeli state of apartheid that "in some ways has been crueler in Israel" than in South Africa because "the entire judicial system conceals and cleanses the praxis of government-led apartheid."[5] Aloni has described the ideology and actions of the state of Israel as racist and has called to replace the ideology of a false "Jewish democracy" with a binational state for all people from the Jordan river to the Mediterranean sea[6] He supports the BDS (Boycott, Divestment and Sanctions) movement because it is a means for equal dialogue and because it creates a space for nonviolent resistance. He views Palestinians as a "brother ... with whom I share a common identity."[7] The slogan "From the River to the Sea all People Must be Free" appears on Aloni's website.[8]

The film Forgiveness (2006), which had its Middle-Eastern premiere in Ramallah, recently stirred up controversy when the Israeli embassy in Paris threatened to withdraw funding from the Israeli Film Festival in Paris (du Film – Israelien de Paris) should they open the festival with the film.[9] Aloni (along with Naomi Klein, John Greyson, and others) was an initiator of the Toronto Declaration,.[10]

In all of his work, Aloni aims at "promoting justice, peace, solidarity and love between Israel and Palestine."[8]